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Trait-associated genetic variants affect complex phenotypes primarily via regulatory mechanisms on the transcriptome. To investigate the genetics of gene expression, we performed cis- and trans-expression quantitative trait locus (eQTL) analyses using blood-derived expression from 31,684 individuals through the eQTLGen Consortium. We detected cis-eQTL for 88% of genes, and these were replicable in numerous tissues. Distal trans-eQTL (detected for 37% of 10,317 trait-associated variants tested) showed lower replication rates, partially due to low replication power and confounding by cell type composition. However, replication analyses in single-cell RNA-seq data prioritized intracellular trans-eQTL. Trans-eQTL exerted their effects via several mechanisms, primarily through regulation by transcription factors. Expression of 13% of the genes correlated with polygenic scores for 1,263 phenotypes, pinpointing potential drivers for those traits. In summary, this work represents a large eQTL resource, and its results serve as a starting point for in-depth interpretation of complex phenotypes.

The efficient healing of critical-sized bone defects using synthetic biomaterial-based strategies is promising but remains challenging as it requires the development of biomaterials that combine a 3D porous architecture and a robust biological activity. Bioactive glasses (BGs) are attractive candidates as they stimulate a biological response that favors osteogenesis and vascularization, but amorphous 3D porous BGs are difficult to produce because conventional compositions crystallize during processing. Here, we rationally designed a porous, strontium-releasing, bioactive glass-based scaffold (pSrBG) whose composition was tailored to deliver strontium and whose properties were optimized to retain an amorphous phase, induce tissue infiltration and encourage bone formation. The hypothesis was that it would allow the repair of a critical-sized defect in an ovine model with newly-formed bone exhibiting physiological matrix composition and structural architecture. Histological and histomorphometric analyses combined with indentation testing showed pSrBG encouraged near perfect bone-to-material contact and the formation of well-organized lamellar bone. Analysis of bone quality by a combination of Raman spectral imaging, small-angle X-ray scattering, X-ray fluorescence and focused ion beam-scanning electron microscopy demonstrated that the repaired tissue was akin to that of normal, healthy bone, and incorporated small amounts of strontium in the newly formed bone mineral. These data show the potential of pSrBG to induce an efficient repair of critical-sized bone defects and establish the importance of thorough multi-scale characterization in assessing biomaterial outcomes in large animal models.

We use a genome-wide association of 1 million parental lifespans of genotyped subjects and data on mortality risk factors to validate previously unreplicated findings near CDKN2B-AS1, ATXN2/BRAP, FURIN/FES, ZW10, PSORS1C3, and 13q21.31, and identify and replicate novel findings near ABO, ZC3HC1, and IGF2R. We also validate previous findings near 5q33.3/EBF1 and FOXO3, whilst finding contradictory evidence at other loci. Gene set and cell-specific analyses show that expression in foetal brain cells and adult dorsolateral prefrontal cortex is enriched for lifespan variation, as are gene pathways involving lipid proteins and homeostasis, vesicle-mediated transport, and synaptic function. Individual genetic variants that increase dementia, cardiovascular disease, and lung cancer – but not other cancers – explain the most variance. Resulting polygenic scores show a mean lifespan difference of around five years of life across the deciles. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter)., eLife digest Ageing happens to us all, and as the cabaret singer Maurice Chevalier pointed out, "old age is not that bad when you consider the alternative". Yet, the growing ageing population of most developed countries presents challenges to healthcare systems and government finances. For many older people, long periods of ill health are part of the end of life, and so a better understanding of ageing could offer the opportunity to prolong healthy living into old age. Ageing is complex and takes a long time to study – a lifetime in fact. This makes it difficult to discern its causes, among the countless possibilities based on an individual’s genes, behaviour or environment. While thousands of regions in an individual’s genetic makeup are known to influence their risk of different diseases, those that affect how long they will live have proved harder to disentangle. Timmers et al. sought to pinpoint such regions, and then use this information to predict, based on their DNA, whether someone had a better or worse chance of living longer than average. The DNA of over 500,000 people was read to reveal the specific ‘genetic fingerprints’ of each participant. Then, after asking each of the participants how long both of their parents had lived, Timmers et al. pinpointed 12 DNA regions that affect lifespan. Five of these regions were new and had not been linked to lifespan before. Across the twelve as a whole several were known to be involved in Alzheimer’s disease, smoking-related cancer or heart disease. Looking at the entire genome, Timmers et al. could then predict a lifespan score for each individual, and when they sorted participants into ten groups based on these scores they found that top group lived five years longer than the bottom, on average. Many factors beside genetics influence how long a person will live and our lifespan cannot be read from our DNA alone. Nevertheless, Timmers et al. had hoped to narrow down their search and discover specific genes that directly influence how quickly people age, beyond diseases. If such genes exist, their effects were too small to be detected in this study. The next step will be to expand the study to include more participants, which will hopefully pinpoint further genomic regions and help disentangle the biology of ageing and disease.

Genome-wide association studies (GWAS) have identified thousands of variants associated with complex traits, but their biological interpretation often remains unclear. Most of these variants overlap with expression QTLs, indicating their potential involvement in regulation of gene expression. Here, we propose a transcriptome-wide summary statistics-based Mendelian Randomization approach (TWMR) that uses multiple SNPs as instruments and multiple gene expression traits as exposures, simultaneously. Applied to 43 human phenotypes, it uncovers 3,913 putatively causal gene–trait associations, 36% of which have no genome-wide significant SNP nearby in previous GWAS. Using independent association summary statistics, we find that the majority of these loci were missed by GWAS due to power issues. Noteworthy among these links is educational attainment-associated BSCL2, known to carry mutations leading to a Mendelian form of encephalopathy. We also find pleiotropic causal effects suggestive of mechanistic connections. TWMR better accounts for pleiotropy and has the potential to identify biological mechanisms underlying complex traits.

Type 2 diabetes (T2D) is a very common disease in humans. Here we conduct a meta-analysis of genome-wide association studies (GWAS) with ~16 million genetic variants in 62,892 T2D cases and 596,424 controls of European ancestry. We identify 139 common and 4 rare variants associated with T2D, 42 of which (39 common and 3 rare variants) are independent of the known variants. Integration of the gene expression data from blood (n = 14,115 and 2765) with the GWAS results identifies 33 putative functional genes for T2D, 3 of which were targeted by approved drugs. A further integration of DNA methylation (n = 1980) and epigenomic annotation data highlight 3 genes (CAMK1D, TP53INP1, and ATP5G1) with plausible regulatory mechanisms, whereby a genetic variant exerts an effect on T2D through epigenetic regulation of gene expression. Our study uncovers additional loci, proposes putative genetic regulatory mechanisms for T2D, and provides evidence of purifying selection for T2D-associated variants., GWAS have so far identified 129 loci associated with type 2 diabetes (T2D). Here, the authors meta-analyse three large T2D GWA studies which uncovers 42 additional loci, further prioritize 33 functional genes using eQTL and mQTL data and propose regulatory mechanisms for three putative T2D genes.

Thulium fiber laser lithotripsy using smaller optical fibers may enable development of miniature ureteroscopes. Two ureteroscope distal tip prototypes were built and characterized. The first design was 4.5-French (Fr) [1.5-mm outer diameter (OD)], five channel tip, housing 200-μm inner diameter (ID) dedicated central channel for insertion of 100-μm core fibers and four surrounding channels, each with 1.5 Fr (510-μm ID) for instrumentation, irrigation, imaging, and illumination, respectively. The second design was 6.0-Fr (2.0-mm OD), three-dimensional printed tip with larger, hemispherical common working channel and separate detection port integrated with ring lighting. Standard instruments, including optical fibers, guidewires, and stone baskets, were inserted through working channels to demonstrate feasibility. Gravitational and manual pump-assisted saline irrigation rates were measured. Luminous intensity distribution curves (LIDCs) were modeled for both ring and conventional lighting designs. Imaging was conducted using 3000, 6000, and 10,000 pixel, miniature, flexible endoscopes with 0.4-, 0.6-, and 0.9-mm OD, to differentiate between urinary stones and ureter wall, for potential clinical application. The multichannel ureteroscope tip with 1.5-Fr working channel yielded a gravitational saline flow rate of 3.9 ± 0.2 mL / min compared to 31.3 ± 0.6 mL / min for standard (3.6 Fr) ureteroscope channel. Manual, pump-assisted irrigation increased flow rate to 32.5 ± 3.0 mL / min. The 6000 pixel, 0.6-mm OD, flexible endoscope provided a balance of clear differentiation between stones and ureter wall and sufficiently small OD. A ring lighting configuration provided more uniform illumination than conventional cross-lighting geometry as demonstrated by LIDCs. With further development, these miniature ureteroscope tip designs may be integrated into a fully functional ureteroscope to permit ureteral access with minimal trauma and improved patient safety and comfort.

Optical fibers, consisting of 240-μm-core trunk fibers with rounded, 450-μm-diameter ball tips, are currently used during Holmium:YAG laser lithotripsy to reduce mechanical damage to the inner lining of the ureteroscope working channel during fiber insertion and prolong ureteroscope lifetime. Similarly, this study tests a smaller, 100-μm-core fiber with 300-μm-diameter ball tip during thulium fiber laser (TFL) lithotripsy. TFL was operated at a wavelength of 1908 nm, with 35-mJ pulse energy, 500-μs pulse duration, and 300-Hz pulse rate. Calcium oxalate/phosphate stone samples were weighed, laser procedure times were measured, and ablation rates were calculated for ball tip fibers, with comparison to bare tip fibers. Photographs of ball tips were taken before and after each procedure to track ball tip degradation and determine number of procedures completed before need for replacement. A high speed camera also recorded the cavitation bubble dynamics during TFL lithotripsy. Additionally, saline irrigation rates and ureteroscope deflection were measured with and without the presence of TFL fiber. There was no statistical difference (P>0.05) between stone ablation rates for single-use ball tip fiber (1.3±0.4 mg/s) (n=10), multiple-use ball tip fiber (1.3±0.5 mg/s) (n=44), and conventional single-use bare tip fibers (1.3±0.2 mg/s) (n=10). Ball tip durability varied widely, but fibers averaged greater than four stone procedures before failure, defined by rapid decline in stone ablation rates. Mechanical damage at the front surface of the ball tip was the limiting factor in fiber lifetime. The small fiber diameter did not significantly impact ureteroscope deflection or saline flow rates. The miniature ball tip fiber may provide a cost-effective design for safe fiber insertion through the ureteroscope working channel and into the ureter without risk of instrument damage or tissue perforation, and without compromising stone ablation efficiency during TFL lithotripsy.

The experimental thulium fiber laser (TFL) is being explored as an alternative to the current clinical gold standard Holmium:YAG laser for lithotripsy. The near single-mode TFL beam allows coupling of higher power into smaller optical fibers than the multimode Holmium laser beam profile, without proximal fiber tip degradation. A smaller fiber is desirable because it provides more space in the ureteroscope working channel for increased saline irrigation rates and allows maximum ureteroscope deflection. However, distal fiber tip burnback increases as fiber diameter decreases. Previous studies utilizing hollow steel sheaths around recessed distal fiber tips reduced fiber burnback but increased stone retropulsion. A “fiber muzzle brake” was tested for reducing both fiber burnback and stone retropulsion by manipulating vapor bubble expansion. TFL lithotripsy studies were performed at 1908 nm, 35 mJ, 500 ?? ? s , and 300 Hz using a 100 - ? m -core fiber. The optimal stainless steel muzzle brake tip tested consisted of a 1-cm-long, 560 - ? m -outer-diameter, 360 - ? m -inner-diameter tube with a 275 - ? m -diameter through hole located 250 ?? ? m from the distal end. The fiber tip was recessed a distance of 500 ?? ? m . Stone phantom retropulsion, fiber tip burnback, and calcium oxalate stone ablation studies were performed ex vivo. Small stones with a mass of 40 ± 4 ?? mg and 4-mm-diameter were ablated over a 1.5-mm sieve in 25 ± 4 ?? s

Using a validated in vitro ureter model for laser lithotripsy, the performance of an experimental thulium fiber laser (TFL) was studied and compared to the clinical gold standard holmium:YAG laser. The holmium laser (λ = 2120 nm) was operated with standard parameters of 600 mJ, 350 μs, 6 Hz, and 270-μm-core optical fiber. The TFL (λ=1908 nm) was operated with 35 mJ, 500 μs, 150 to 500 Hz, and a 100-μm-core fiber. Urinary stones (60% calcium oxalate monohydrate/40% calcium phosphate) of uniform mass and diameter (4 to 5 mm) were laser ablated with fibers through a flexible video-ureteroscope under saline irrigation with flow rates of 22.7 and 13.7 ml/ min for the TFL and holmium laser, respectively. The temperature 3 mm from the tube's center and 1 mm above the mesh sieve was measured by a thermocouple and recorded throughout each experiment for both lasers. Total laser and operation times were recorded once all stone fragments passed through a 1.5-mm sieve. The holmium laser time measured 167±41 s (n=12). TFL times measured 111±49, 39±11, and 23±4 s, for pulse rates of 150, 300, and 500 Hz, respectively (n=12 each). Mean peak saline irrigation temperatures reached 24±1°C for holmium, and 33±3°C, 33±7°C, and 39±6°C, for TFL at pulse rates of 150, 300, and 500 Hz, respectively. To avoid thermal buildup and provide a sufficient safety margin, TFL lithotripsy should be performed with pulse rates below 500 Hz and/or increased saline irrigation rates. The TFL rapidly fragmented kidney stones due in part to its high pulse rate, high power density, high average power, and observation of reduced stone retropulsion and may provide a clinical alternative to the conventional holmium laser for lithotripsy.

The yeast scaffold protein Pan1 contains two EH domains at its N-terminus, a predicted coiled-coil central region, and a C-terminal proline-rich domain. Pan1 is also predicted to contain regions of intrinsic disorder, characteristic of proteins that have many binding partners. In vitro biochemical data suggest that Pan1 exists as a dimer, and we have identified amino acids 705 to 848 as critical for this homotypic interaction. Tryptophan fluorescence was used to further characterize Pan1 conformational states. Pan1 contains four endogenous tryptophans, each in a distinct region of the protein: Trp(312) and Trp(642) are each in an EH domain, Trp(957) is in the central region, and Trp(1280) is a critical residue in the Arp2/3 activation domain. To examine the local environment of each of these tryptophans, three of the four tryptophans were mutagenized to phenylalanine to create four proteins, each with only one tryptophan residue. When quenched with acrylamide, these single tryptophan mutants appeared to undergo collisional quenching exclusively and were moderately accessible to the acrylamide molecule. Quenching with iodide or cesium, however, revealed different Stern-Volmer constants due to unique electrostatic environments of the tryptophan residues. Time-resolved fluorescence anisotropy data confirmed structural and disorder predictions of Pan1. Further experimentation to fully develop a model of Pan1 conformational dynamics will assist in a deeper understanding of the mechanisms of endocytosis.

The use of thulium fiber laser (TFL) as a potential alternative laser lithotripter to the clinical holmium:YAG laser is being studied. The TFL’s Gaussian spatial beam profile provides efficient coupling of higher laser power into smaller core fibers without proximal fiber tip degradation. Smaller fiber diameters are more desirable, because they free up space in the single working channel of the ureteroscope for increased saline irrigation rates and allow maximum ureteroscope deflection. However, distal fiber tip degradation and “burn-back” increase as fiber diameter decreases due to both excessive temperatures and mechanical stress experienced during stone ablation. To eliminate fiber tip burn-back, the distal tip of a 150-μm core silica fiber was glued inside 1-cm-long steel tubing with fiber tip recessed 100, 250, 500, 1000, or 2000 μm inside the steel tubing to create the hollow-tip fiber. TFL pulse energy of 34 mJ with 500-μs pulse duration and 150-Hz pulse rate was delivered through the hollow-tip fibers in contact with human calcium oxalate monohydrate urinary stones during ex vivo studies. Significant fiber tip burn-back and degradation was observed for bare 150-μm core-diameter fibers. However, hollow steel tip fibers experienced minimal fiber burn-back without compromising stone ablation rates. A simple, robust, compact, and inexpensive hollow fiber tip design was characterized for minimizing distal fiber burn-back during the TFL lithotripsy. Although an increase in stone retropulsion was observed, potential integration of the hollow fiber tip into a stone basket may provide rapid stone vaporization, while minimizing retropulsion.

The thulium fiber laser (TFL) is currently being studied as an alternative to the conventional holmium:YAG (Ho:YAG) laser for lithotripsy. The diode-pumped TFL may be electronically modulated to operate with variable parameters (e.g., pulse rate, pulse duration, and duty cycle) for studying the influence of pulse train mode on stone ablation rates. The TFL under study was operated at 1908 nm, 35-mJ pulse energy, and 500-μs pulse duration, in a train of 5 micro-pulses, with macro-pulse rates of 10 Hz, compared with conventional TFL operation at 10 to 50 Hz. TFL energy was delivered through 100-μm-core fibers in contact with human uric acid (UA) and calcium oxalate monohydrate (COM) stones. Mass removal rates, optical coherence tomography, and light microscopy were used to analyze the ablation craters. Stone retropulsion and fiber tip degradation studies also were conducted for these laser parameters. TFL operation in micro-pulse train (MPT) mode resulted in a factor of two increase in the ablation rate of 414 ± 94 μg/s and 122 ± 24 μg/s for the UA and COM stones, respectively, compared to 182 ± 69 μg/s and 60 ± 14 μg/s with standard pulse trains delivered at 50 Hz (P0.05). Stone retropulsion remained minimal (2 mm after 1200 pulses) for both pulse modes. Fiber burnback was significant for both pulse modes and was higher for COM stones than UA stones. TFL operation in MPT mode results in increased stone ablation rates which, with further optimization, may approach levels comparable to Ho:YAG laser lithotripsy in the clinic.

The thulium fiber laser (TFL) has recently been proposed as an alternative to the Holmium:YAG (Ho:YAG) laser for lithotripsy. The TFL's Gaussian spatial beam profile provides higher power transmission through smaller optical fibers with reduced proximal fiber tip damage, and improved saline irrigation and flexibility through the ureteroscope. However, distal fiber tip damage may still occur during stone fragmentation, resulting in disposal of the entire fiber after the procedure. A novel design for a short, detachable, distal fiber tip that can fit into an ureteroscope's working channel is proposed. A prototype, twist-lock, spring-loaded mechanism was constructed using micromachining methods, mating a 150-μm-core trunk fiber to 300-μm-core fiber tip. Optical transmission measuring 80% was observed using a 30-mJ pulse energy and 500-μs pulse duration. Ex vivo human calcium oxalate monohydrate urinary stones were vaporized at an average rate of 187 μg/s using 20-Hz modulated, 50% duty cycle 5 pulse packets. The highest stone ablation rates corresponded to the highest fiber tip degradation, thus providing motivation for use of detachable and disposable distal fiber tips during lithotripsy. The 1-mm outer-diameter prototype also functioned comparable to previously tested tapered fiber tips.

Fiber-optic attraction of urinary stones during laser lithotripsy may be exploited to manipulate stone fragments inside the urinary tract without mechanical grasping tools, saving the urologist time and space in the ureteroscope working channel. We compare thulium fiber laser (TFL) high pulse rate/low pulse energy operation to conventional holmium:YAG low pulse rate/high pulse energy operation for fiber-optic suctioning of plaster-of-paris (PoP) stone phantoms. A TFL (wavelength of 1908 nm, pulse energy of 35 mJ, pulse duration of 500 μs, and pulse rate of 10 to 350 Hz) and a holmium laser (wavelength of 2120 nm, pulse energy of 35 to 360 mJ, pulse duration of 300 μs, and pulse rate of 20 Hz) were tested using 270-μm-core optical fibers. A peak drag speed of ~2.5 mm/s was measured for both TFL (35 mJ and 150 to 250 Hz) and holmium laser (210 mJ and 20 Hz). Particle image velocimetry and thermal imaging were used to track water flow for all parameters. Fiber-optic suctioning of urinary stone phantoms is feasible. TFL operation at high pulse rates/low pulse energies is preferable to holmium operation at low pulse rates/high pulse energies for rapid and smooth stone pulling. With further development, this novel technique may be useful for manipulating stone fragments in the urinary tract.